Microbial granules were developed at different substrate N/COD ratios in sequencing batch reactors (SBR). Results showed that heterotrophic, nitrifying, and denitrifying populations could peacefully co-exist in microbial granules, while increased substrate N/COD ratio led to significant shifts among three populations in granules. Enhanced activities of nitrifying and denitrifying populations were obtained in microbial granules developed at high substrate N/COD ratios, however, heterotrophic populations in granules tended to decrease with the increase of substrate N/COD ratio. It was found that dissolved oxygen (DO) concentration had a pronounced effect on the efficiency of denitrification by microbial granules, meanwhile the results also indicated that a certain mixing power would be provided to ensure mass transfer between liquid and granules during denitrification. It was demonstrated that complete organics and nitrogen removal can be achieved in single granule-based SBR with high efficiency and stable performance. This is the first study to show the capability of microbial granules in simultaneous removal of organic carbon and nitrogen from wastewater.